Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels.

Designing diagnostic assays to genotype rapidly mutating viruses remains a challenge despite the overall improvements in nucleic acid detection technologies. RT-PCR and next-generation sequencing are unsuitable for genotyping during outbreaks or in point-of-care detection due to their infrastructure requirements and longer turnaround times. We developed a quantum dot barcode multiplexing system to genotype mutated viruses. We designed multiple quantum dot barcodes to target conserved, wildtype, and mutated regions of SARS-CoV-2. We calculated ratios of the signal output from different barcodes that enabled SARS-CoV-2 detection and identified SARS-CoV-2 variant strains from a sample. We detected different sequence types, including conserved genes, nucleotide deletions, and single nucleotide substitutions. Our system detected SARS-CoV-2 patient specimens with 98% sensitivity and 94% specificity across 91 patient samples. Further, we leveraged our barcoding and ratio system to track the emergence of the N501Y SARS-CoV-2 mutation from December 2020 to May 2021 and demonstrated that the more transmissible N501Y mutation started to dominate infections by April 2021. Our barcoding and signal ratio approach can genotype viruses and track the emergence of viral mutations in a single diagnostic test. This technology can be extended to tracking other viruses. Combined with smartphone detection technologies, this assay can be adapted for point-of-care tracking of viral mutations in real time.

Surface and Air Contamination With Severe Acute Respiratory Syndrome Coronavirus 2 From Hospitalized Coronavirus Disease 2019 Patients in Toronto, Canada, March-May 2020.

BACKGROUND: We determined the burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in air and on surfaces in rooms of patients hospitalized with coronavirus disease 2019 (COVID-19) and investigated patient characteristics associated with SARS-CoV-2 environmental contamination. METHODS: Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at 6 acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 ribonucleic acid (RNA), cultured to determine potential infectivity, and whole viral genomes were sequenced. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated. RESULTS: Severe acute respiratory syndrome coronavirus 2 RNA was detected from surfaces (125 of 474 samples; 42 of 78 patients) and air (3 of 146 samples; 3 of 45 patients); 17% (6 of 36) of surface samples from 3 patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, polymerase chain reaction-positive nasopharyngeal swab (cycle threshold of ≤30) on or after surface sampling date, higher Charlson comorbidity score, and shorter time from onset of illness to sampling date were significantly associated with detection of SARS-CoV-2 RNA in surface samples. CONCLUSIONS: The infrequent recovery of infectious SARS-CoV-2 virus from the environment suggests that the risk to healthcare workers from air and near-patient surfaces in acute care hospital wards is likely limited.

Paediatric Burkitt lymphoma patient-derived xenografts capture disease characteristics over time and are a model for therapy.

Burkitt lymphoma (BL) accounts for almost two-thirds of all B-cell non-Hodgkin lymphoma (B-NHL) in children and adolescents and is characterised by a MYC translocation and rapid cell turnover. Intensive chemotherapeutic regimens have been developed in recent decades, including the lymphomes malins B (LMB) protocol, which have resulted in a survival rate in excess of 90%. Recent clinical trials have focused on immunochemotherapy, with the addition of rituximab to chemotherapeutic backbones, showing encouraging results. Despite these advances, relapse and refractory disease occurs in up to 10% of patients and salvage options for these carry a dismal prognosis. Efforts to better understand the molecular and functional characteristics driving relapse and refractory disease may help improve this prognosis. This study has established a paediatric BL patient-derived xenograft (PDX) resource which captures and maintains tumour heterogeneity, may be used to better characterise tumours and identify cell populations responsible for therapy resistance.

Inhibition of monocarboxyate transporter 1 by AZD3965 as a novel therapeutic approach for diffuse large B-cell lymphoma and Burkitt lymphoma.

Inhibition of monocarboxylate transporter 1 has been proposed as a therapeutic approach to perturb lactate shuttling in tumor cells that lack monocarboxylate transporter 4. We examined the monocarboxylate transporter 1 inhibitor AZD3965, currently in phase I clinical studies, as a potential therapy for diffuse large B-cell lymphoma and Burkitt lymphoma. Whilst extensive monocarboxylate transporter 1 protein was found in 120 diffuse large B-cell lymphoma and 10 Burkitt lymphoma patients' tumors, monocarboxylate transporter 4 protein expression was undetectable in 73% of the diffuse large B-cell lymphoma samples and undetectable or negligible in each Burkitt lymphoma sample. AZD3965 treatment led to a rapid accumulation of intracellular lactate in a panel of lymphoma cell lines with low monocarboxylate transporter 4 protein expression and potently inhibited their proliferation. Metabolic changes induced by AZD3965 in lymphoma cells were consistent with a feedback inhibition of glycolysis. A profound cytostatic response was also observed in vivo: daily oral AZD3965 treatment for 24 days inhibited CA46 Burkitt lymphoma growth by 99%. Continuous exposure of CA46 cells to AZD3965 for 7 weeks in vitro resulted in a greater dependency upon oxidative phosphorylation. Combining AZD3965 with an inhibitor of mitochondrial complex I (central to oxidative phosphorylation) induced significant lymphoma cell death in vitro and reduced CA46 disease burden in vivo These data support clinical examination of AZD3965 in Burkitt lymphoma and diffuse large B-cell lymphoma patients with low tumor monocarboxylate transporter 4 expression and highlight the potential of combination strategies to optimally target the metabolic phenotype of tumors.

Store-operated Ca(2+) entry in proliferating and retinoic acid-differentiated N- and S-type neuroblastoma cells.

Neuroblastoma cell lines are heterogeneous, comprised of at least three distinct cell phenotypes; neuroblastic N-type cells, non-neuronal substrate-adherent S-type cells and intermediate I-type cells. N- and S-type cell populations were enriched from the parental SH-SY5Y neuroblastoma cell line and induced to differentiate by the addition of retinoic acid (RA), a drug used in the treatment of neuroblastoma. N- and S-type cells were identified based on their differential expression of ß-tubulin III, vimentin and Bcl-2. Store-operated Ca(2+) entry (SOCE) was then measured in proliferating and differentiated N- and S-type cell populations and the expression of STIM1, Orai1 and TRPC1, three proteins reported to play a key role in SOCE, was determined. In N-type cells the RA-induced switch from proliferation to differentiation was accompanied by a down-regulation in SOCE. STIM1 and Orai1 expression became down-regulated in differentiated cells, consistent with their respective roles as ER Ca(2+) sensor and store-operated Ca(2+) channel (SOC). TRPC1 became up-regulated suggesting that TRPC1 is not involved in SOCE, at least in differentiated N-type cells. In S-type cells SOCE remained active following the RA-induced switch from proliferation to differentiation and the expression of STIM1 and Orai1 remained unchanged. TRPC1 was not expressed in S-type cells. Our results indicate that differentiation of neuronal cells is associated with a remodelling of SOCE. Therapeutic targeting of SOCE proteins could potentially be a means of promoting neuronal differentiation in the treatment of neuroblastoma.

Addressing CAUTIs with an External Female Catheter.

BACKGROUND: Catheter-associated urinary tract infections (CAUTIs) can lead to complications that prolong hospital stays and result in patient discomfort as well as increased health care costs and mortality. At our academic medical center in New York City, in 2016-17, 21 of 87 CAUTI cases (24%) were in bedbound female patients in whom indwelling catheters were used for incontinence. Although condom catheters were available as an alternative to indwelling urinary catheters for male patients, there was a lack of effective products for female patients. METHODS: A team of clinical nurse specialists (CNSs) conducted a literature search, reviewed internal data on CAUTI rates and catheter use, and searched for available catheter alternatives that would meet the needs of bedbound female patients. The team identified two different external female urinary catheters and piloted both with a focus on efficacy as well as stakeholder satisfaction. RESULTS: In 2019-20, external female catheters were used in 1,195 unique patients. Approximately 90% of external female catheter use was to avoid using an indwelling urinary catheter. With a cost avoidance of $13,786 per patient, $16,473,912 in costs to the organization were avoided. CAUTI rates in bedbound female patients decreased after implementation of the external female catheters. CONCLUSION: This initiative demonstrates that external female urinary catheters can be used at other hospitals to decrease indwelling urinary catheter use and CAUTI rates in bedbound female patients.

Coaching for impact: successful implementation of a multi-national, multi-institutional synchronous research course in Ethiopia.

Purpose: Under the American College of Surgeons' Operation Giving Back, several US institutions collaborated with a teaching and regional referral hospital in Ethiopia to develop a surgical research curriculum. Methods: A virtual, interactive, introductory research course which utilized a web-based classroom platform and live educational sessions via an online teleconferencing application was implemented. Surgical and public health faculty from the US and Ethiopia taught webinars and led breakout coaching sessions to facilitate participants' project development. Both a pre-course needs assessment survey and a post-course participation survey were used to examine the impact of the course. Results: Twenty participants were invited to participate in the course. Despite the majority of participants having connection issues (88%), 11 participants completed the course with an 83% average attendance rate. Ten participants successfully developed structured research proposals based on their local clinical needs. Conclusion: This novel multi-institutional and multi-national research course design was successfully implemented and could serve as a template for greater development of research capacity building in the low- and middle-income country (LMIC) setting.

A Colorimetric Test to Differentiate Patients Infected with Influenza from COVID-19.

Patients infected with SARS-CoV-2 and influenza display similar symptoms, but treatment requirements are different. Clinicians need to accurately distinguish SARS-CoV-2 from influenza to provide appropriate treatment. Here, the authors develope a color-based technique to differentiate between patients infected with SARS-CoV-2 and influenza A using a nucleic acid enzyme-gold nanoparticle (GNP) molecular test requiring minimal equipment. The MNAzyme and GNP probes are designed to be robust to viral mutations. Conserved regions of the viral genomes are targeted, and two MNAzymes are created for each virus. The ability of the system to distinguish between SARS-CoV-2 and influenza A using 79 patient samples is tested. When detecting SARS-CoV-2 positive patients, the clinical sensitivity is 90%, and the specificity is 100%. When detecting influenza A, the clinical sensitivity and specificity are 93% and 100%, respectively. The high clinical performance of the MNAzyme-GNP assay shows that it can be used to help clinicians choose effective treatments.

Nitrosative Stress and Lipid Homeostasis as a Mechanism for Zileuton Hepatotoxicity and Resistance in Genetically Sensitive Mice.

Zileuton is an orally active inhibitor of leukotriene synthesis for maintenance treatment of asthma, for which clinical usage has been associated with idiosyncratic liver injury. Mechanistic understanding of zileuton toxicity is hampered by the rarity of the cases and lack of an animal model. A promising model for mechanistic study of rare liver injury is the Diversity Outbred (J:DO) mouse population, with genetic variation similar to that found in humans. In this study, female DO mice were administered zileuton or vehicle daily for 7 days (i.g.). Serum liver enzymes were elevated in the zileuton group, with marked interindividual variability in response. Zileuton exposure-induced findings in susceptible DO mice included microvesicular fatty change, hepatocellular mitosis, and hepatocellular necrosis. Inducible nitric oxide synthase and nitrotyrosine abundance were increased in livers of animals with necrosis and those with fatty change, implicating nitrosative stress as a possible injury mechanism. Conversely, DO mice lacking adverse liver pathology following zileuton exposure experienced decreased hepatic concentrations of resistin and increased concentrations of insulin and leptin, providing potential clues into mechanisms of toxicity resistance. Transcriptome pathway analysis highlighted mitochondrial dysfunction and altered fatty acid oxidation as key molecular perturbations associated with zileuton exposure, and suggested that interindividual differences in cytochrome P450 metabolism, glutathione-mediated detoxification, and farnesoid X receptor signaling may contribute to zileuton-induced liver injury (ZILI). Taken together, DO mice provided a platform for investigating mechanisms of toxicity and resistance in context of ZILI which may lead to targeted therapeutic interventions.

Use of Disinfection Cap to Reduce Central-Line-Associated Bloodstream Infection and Blood Culture Contamination Among Hematology-Oncology Patients.

OBJECTIVE: In this study, we examined the impact of routine use of a passive disinfection cap for catheter hub decontamination in hematology-oncology patients. SETTING: A tertiary care cancer center in New York City. METHODS: In this multiphase prospective study, we used 2 preintervention phases (P1 and P2) to establish surveillance and baseline rates followed by sequential introduction of disinfection caps on high-risk units (HRUs: hematologic malignancy wards, hematopoietic stem cell transplant units and intensive care units) (P3) and general oncology units (P4). Unit-specific and hospital-wide hospital-acquired central-line-associated bloodstream infection (HA-CLABSI) rates and blood culture contamination (BCC) with coagulase negative staphylococci (CONS) were measured. RESULTS: Implementation of a passive disinfection cap resulted in a 34% decrease in hospital-wide HA-CLABSI rates (combined P1 and P2 baseline rate of 2.66-1.75 per 1,000 catheter days at the end of the study period). This reduction occurred only among high-risk patients and not among general oncology patients. In addition, the use of the passive disinfection cap resulted in decreases of 63% (HRUs) and 51% (general oncology units) in blood culture contamination, with an estimated reduction of 242 BCCs with CONS. The reductions in HA-CLABSI and BCC correspond to an estimated annual savings of $3.2 million in direct medical costs. CONCLUSION: Routine use of disinfection caps is associated with decreased HA-CLABSI rates among high-risk hematology oncology patients and a reduction in blood culture contamination among all oncology patients.

Identifying research priorities in anaesthesia and perioperative care: final report of the joint National Institute of Academic Anaesthesia/James Lind Alliance Research Priority Setting Partnership.

OBJECTIVE: To identify research priorities for Anaesthesia and Perioperative Medicine. DESIGN: Prospective surveys and consensus meetings guided by an independent adviser. SETTING: UK. PARTICIPANTS: 45 stakeholder organisations (25 professional, 20 patient/carer) affiliated as James Lind Alliance partners. OUTCOMES: First 'ideas-gathering' survey: Free text research ideas and suggestions. Second 'prioritisation' survey: Shortlist of 'summary' research questions (derived from the first survey) ranked by respondents in order of priority. Final 'top ten': Agreed by consensus at a final prioritisation workshop. RESULTS: First survey: 1420 suggestions received from 623 respondents (49% patients/public) were refined into a shortlist of 92 'summary' questions. Second survey: 1718 respondents each nominated up to 10 questions as research priorities. Top ten: The 25 highest-ranked questions advanced to the final workshop, where 23 stakeholders (13 professional, 10 patient/carer) agreed the 10 most important questions: ▸ What can we do to stop patients developing chronic pain after surgery? ▸ How can patient care around the time of emergency surgery be improved? ▸ What long-term harm may result from anaesthesia, particularly following repeated anaesthetics?▸ What outcomes should we use to measure the 'success' of anaesthesia and perioperative care? ▸ How can we improve recovery from surgery for elderly patients? ▸ For which patients does regional anaesthesia give better outcomes than general anaesthesia? ▸ What are the effects of anaesthesia on the developing brain? ▸ Do enhanced recovery programmes improve short and long-term outcomes? ▸ How can preoperative exercise or fitness training, including physiotherapy, improve outcomes after surgery? ▸ How can we improve communication between the teams looking after patients throughout their surgical journey? CONCLUSIONS: Almost 2000 stakeholders contributed their views regarding anaesthetic and perioperative research priorities. This is the largest example of patient and public involvement in shaping anaesthetic and perioperative research to date.

Metal ion complexes of EDTA as solutes for density gradient ultracentrifugation: influence of metal ions.

In the study reported here, we study the nature of the metal ion complexes of EDTA as solute systems for analysis of lipoproteins by density gradient ultracentrifugation (DGU) by varying both the complexing metal ion and the counterion. Specifically, the sodium and cesium salts of complexes of Bi/EDTA, Pb/EDTA, Cd/EDTA, Fe/EDTA, and Cu/EDTA were chosen for this study. We show that useful gradients can be formed within a few hours beginning with a homogeneous solution. Data are presented that provide insight into the nature of how these gradients are formed from these complexes and how the selection of a specific complex can be used to enhance particular regions of the lipoprotein density profile for clinical studies. We also examine the use of equilibrium sedimentation theory to correlate the measured density profiles generated by these complexes with their molecular weight.